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Assessing the Genetic Diversity of Rice Originating from Bangladesh, Assam and West Bengal

Anthony J. Travis
Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 3UU, UK

Gareth J. Norton
Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 3UU, UK

Sutapa Datta
Department of Genetics, ICAR-Indian AgriculturalResearch Institute, New Delhi, India

Ramendra Sarma
Department of Plant Breeding andGenetics, Assam Agricultural University, Jorhat 785013, Assam, India

Tapash Dasgupta
Department of Genetics and Plant Breeding, Calcutta University, 35 B.C.Road, Kolkata 700 019, West Bengal, India.

Filipe L. Savio
Luiz de Queiroz College of Agriculture, University of São Paulo, Avenida Pádua Dias, 11, Bairro Agronomia, Piracicaba, São Paulo, Brazil.6

Malcolm Macaulay
Cell & Molecular Sciences, TheJames Hutton Institute, Invergowrie, Dundee DD2 5DA, UK

Peter E. Hedley
Cell & Molecular Sciences, TheJames Hutton Institute, Invergowrie, Dundee DD2 5DA, UK

Kenneth L. McNally
International Rice Research Institute (IRRI), DAPO 7777, Metro Manila 1031, The Philippines

Mahmud H. Sumon
Department of Soil Science, Bangladesh Agricultural University, Mymensingh, Bangladesh.

M. Rafiqul Islam
Department of Soil Science, Bangladesh Agricultural University, Mymensingh, Bangladesh.

Adam H. Price
Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 3UU, UK

Abstract/ Executive Summary:

Background:Genetic diversity among rice cultivars from Bangladesh and North East India was assessed using a custom 384-SNP microarray assay. A total of 511 cultivars were obtained from several sources, choosing landraces likely to be from the aus sub population and modern improved cultivars from Bangladesh. Cultivars from the Oryza SNP set and Rice Diversity Panel 1 (RDP1) were also included for reference. Results: The population analysis program STRUCTURE was used to infer putative population groups in the panel,revealing four groups: indica (76 cultivars), japonica(55) and two distinct groups within the aus subpopulation (aus-1= 99,aus-2 =151). Principal Component Analysis was used to confirm the four population groups identified by STRUCTURE. The analysis revealed cultivars that belonged to neitheraus-1noraus-2but which are clearly aus based on the combined probabilities of their membership of the two aus groups which have been termed aus-admix Information obtained from the panel of 511 cultivars was used to assign rice groups to 74 additional landraces obtained from Assam and West Bengal. While both theaus-1andaus-2groups were represented approximately equally in India,aus-2(which includes cultivar N 22) was more common in Bangladesh, but was not found at all in West Bengal.Conclusions:Examining the distribution of landrace names within theaus-1andaus-2groups suggests thataus-1isassociated with the term “boro”, a word used to describe a winter growing season in Bangladesh and Assam. The information described here has been used to select a population of 300 cultivars for Genome Wide Association studies of the aus rice subpopulation.

Keywords: Rice, SNP, Aus, Boro, Genotype, Ecotype

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End Date:

Program Area: Socio-economic and Policy

Commodity: Rice

Objectives:

Genetic diversity among rice cultivars from Bangladesh and North East India was assessed using a custom 384-SNP microarray assay

Methodology:

laszmann’s group II (aus), which was originally considered to be exclusive to South and West Asia, was described as having a short life cycle and grown under a range of conditions from fully irrigated to upland (Glaszmann, 1987).This work suggested that group II rice encompasses the aus ecotype but also includes some boro ecotype rice. Normally, the term ‘boro’ refers to a growing season in Bangladesh and Assam during December-May (GRiSP, 2013) and also to genetically diverse cultivars grown during this season (Parsonset al., 1999).”aus/ahu”refers to a growing season in Bangladesh and Assam during April-August (GRiSP, 2013) and also to the rice cultivars grown during this season, which are broadcast sown. These aus/ahu rice cultivars are insensitive to photoperiod and are drought tolerant (Khush, 1997). The geographical term aus and the genetic term aus can cause confusion because there is considerable over-lap between boro and aus cultivars at the genetic level,which means the geographical distinction between them is blurred. Most importantly, cultivars grown during the boro or aus seasons may not all be genetically ‘aus’ cultivars. The recently announced 3,000 rice genomes project (Li et al. 2014) refers to a group of aus/boro genotypes, which is the genetic group normally referred to as aus. A total of 208 accessions out of the 3,000 rice genomes are classified as aus/boro, based on 200,000 SNP markers. A subsequent phylogenetic analysis of all 3,000 genome sequences using 376,000 SNP markers also revealed a genetically related group called aus (Alexandrovet al., 2015). In this paper, we refer to genotypes from this group as ‘aus’ using italics to refer to genetic terms and ‘aus’ in normal font for similar geographic or ecotype terms.A recent analysis of 409 rice cultivars indicated that lines from the aus group originate predominantly from areas in Bangladesh and India (Aliet al.,2011). The genetic diversity of the aus and boro ecotypes is large and includes a number of cultivars known for their adaptation to different environments. Cultivar FR 13A, for example, is the flood tolerant donor of the submergence tolerance geneSub1(Xuet al.,2006); Kasalath is the efficient phosphorus up-take donor of the phosphorus starvation tolerance genePstol1(Gamuyaoet al.,2012); Dular is a rice cultivar thathas increased drought resistance, associated with greater root length and root density (Henryet al., 2011); Rayada also has a large root length and high root density (Henryet al.,2011); Black Gora is a rice cultivar with high seedling vigour (Redoña and Mackill, 1996) and deep roots (Shresthaet al.,2014; Al-Shugeairyet al., 2014) and; N22 is a heat tolerant rice cultivar (Jagadishet al.,2008).A number of previous studies have examined the genetic diversity of rice cultivars from Bangladesh (Parsonset al.,1999; Sajibet al., 2012; Hassanet al., 2012). However these studies involved relatively small numbers of genetic markers. Studies of global populations of rice (Aliet al., 2011) using a larger number of markers to capture global rice genetic diversity are limited by the relatively small number of cultivars obtained from specific geographic regions. The aim of this study is to examine the genetic variation of about 500 landraces from the aus and boro ecotypes of rice that fall with in the aus genetic group of rice based on 384 SNP markers and also use the information obtained to identify the genetic background of field-grown cultivars collected from farmers in West Bengal and Assam in India. The cultivars investigated here will be used to establish a panel of aus cultivars for a subsequent genome wide association (GWA) mapping study within a genetically and geographically distinct group of rice genotypes.

Source of Information: Rice (2015) 8:35

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Funding Source:

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Achievement/Findings:

Examining the distribution of landrace names within the aus-1 and aus-2 groups suggests that aus-1 is associated with the term “boro”, a word used to describe a winter growing season in Bangladesh and Assam. The information described here has been used to select a population of 300 cultivars for Genome Wide Association studies of the aus rice subpopulation.

Knowledge Management: Journal